forked from uataq/co2usa_data_synthesis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathco2usa_washington_dc_baltimore_to_netCDF.m
271 lines (233 loc) · 14.8 KB
/
co2usa_washington_dc_baltimore_to_netCDF.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
% clear all
% close all
set(0,'DefaultFigureWindowStyle','docked')
%% Outstanding questions:
fprintf('No outstanding questions as of 2021-04-12:\n')
%% netCDF creation documentation
% Following the Climate Forecasting conventions for netCDF files documented here:
% http://cfconventions.org/
% http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html
%
% Also following the Attribute Convention for Data Discovery version 1.3
% https://wiki.esipfed.org/Attribute_Convention_for_Data_Discovery_1-3
%
% Variables must have a standard_name, a long_name, or both.
% A standard_name is the name used to identify the physical quantity. A standard name contains no whitespace and is case sensitive.
% A long_name has an ad hoc, human readable format.
% A comment can be used to add further detail, but is not required.
%
% Time and date formating follow this convention:
% https://www.edf.org/health/data-standards-date-and-timestamp-guidelines
%
% Data will be archived at the ORNL DAAC:
% https://daac.ornl.gov/PI/
%
%% Creation date
% date_created: The date on which this version of the data was created. Recommended.
date_created_now = datetime(now,'ConvertFrom','datenum','TimeZone','America/Denver'); date_created_now.TimeZone = 'UTC';
date_created_str = datestr(date_created_now,'yyyy-mm-ddThh:MM:ssZ');
% date_issued: The date on which this data (including all modifications) was formally issued (i.e., made available to a wider audience). Suggested.
date_issued_now = datestr(now,'yyyy-mm-dd');
date_issued = datetime(2020,09,21);
date_issued_str = datestr(date_issued,'yyyy-mm-ddThh:MM:ssZ');
% Working folders
if ~exist('currentFolder','var'); currentFolder = pwd; end
if ~exist('readFolder','var'); readFolder = fullfile(currentFolder(1:regexp(currentFolder,'gcloud.utah.edu')+14),'data','co2-usa','data_input'); end
if ~exist('writeFolder','var'); writeFolder = fullfile(currentFolder(1:regexp(currentFolder,'gcloud.utah.edu')+14),'data','co2-usa','synthesis_output'); end
%% City & provider information:
city = 'washington_dc_baltimore';
city_long_name = 'Washington D.C. - Baltimore (Northeast Corridor)';
city_url = 'https://www.nist.gov/topics/northeast-corridor-urban-test-bed';
i = 1;
provider(i).name = 'Anna Karion';
provider(i).address1 = 'National Institute of Standards and Technology';
provider(i).address2 = '100 Bureau Drive';
provider(i).address3 = 'Gaithersburg, MD 20899';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'National Institute of Standards and Technology (NIST)';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0002-6304-3513';
provider(i).parameter = 'Provider has contributed measurements for: ';
i = 2;
provider(i).name = 'James Whetstone';
provider(i).address1 = 'National Institute of Standards and Technology';
provider(i).address2 = '100 Bureau Drive';
provider(i).address3 = 'Gaithersburg, MD 20899';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'National Institute of Standards and Technology (NIST)';
provider(i).email = '[email protected]';
provider(i).orcid = 'https://orcid.org/0000-0002-5139-9176';
provider(i).parameter = 'Provider has contributed measurements for: ';
i=3;
provider(i).name = 'Steve Prinzivalli';
provider(i).address1 = 'Earth Networks Inc.';
provider(i).address2 = '12410 Milestone Center Dr., Suite 300';
provider(i).address3 = 'Germantown, MD 20876';
provider(i).country = 'United States';
provider(i).city = city_long_name;
provider(i).affiliation = 'Earth Networks Inc.';
provider(i).email = '[email protected]';
provider(i).orcid = '';
provider(i).parameter = 'Provider has contributed measurements for: ';
%% Site meta data
clear site % start fresh
site.reference = 'Karion, Anna, William Callahan, Michael Stock, Steve Prinzivalli, Kristal R. Verhulst, Jooil Kim, Peter K. Salameh, Israel Lopez-Coto, and James Whetstone. “Greenhouse Gas Observations from the Northeast Corridor Tower Network.” Earth System Science Data 12, no. 1 (March 25, 2020): 699–717. https://doi.org/10.5194/essd-12-699-2020.';
site.groups = {}; % List of the site "code_species_inletHt"
site.species = {}; % List of the "species"
site.date_issued = date_issued;
site.date_issued_str = datestr(site.date_issued,'yyyy-mm-ddThh:MM:ssZ');
site.date_created_str = date_created_str;
version_folder = 'v20200921';
% Read the latest site info file and loop through it:
[NEC_sites_num,NEC_sites_txt] = xlsread(fullfile(readFolder,city,version_folder,'NEC_sites.csv'));
NEC_sites_txt = NEC_sites_txt(2:end,:); % Removes the header line
NEC_sites_num = NEC_sites_num(1:end,:); % This excludes the header already
i = 1;
for k = 1:size(NEC_sites_num,1)
fns = dir(fullfile(readFolder,city,version_folder,[NEC_sites_txt{k,1},'*.csv']));
if isempty(fns); continue; end % No data for that site
clear('fns_part');
for j = 1:length(fns); fns_part(j,:) = strsplit(fns(j).name,'-'); end
site.codes{1,i} = NEC_sites_txt{k,1};
site.(site.codes{i}).name = NEC_sites_txt{k,1};
site.(site.codes{i}).long_name = NEC_sites_txt{k,4};
site.(site.codes{i}).code = NEC_sites_txt{k,1};
site.(site.codes{i}).inlet_height_long_name = unique(fns_part(:,4))';
for j = 1:length(site.(site.codes{i}).inlet_height_long_name); site.(site.codes{i}).inlet_height{1,j} = ...
str2double(site.(site.codes{i}).inlet_height_long_name{1,j}(regexp(site.(site.codes{i}).inlet_height_long_name{1,j},'[0-9]'))); end
site.(site.codes{i}).in_lat = NEC_sites_num(k,5);
site.(site.codes{i}).in_lon = NEC_sites_num(k,4);
site.(site.codes{i}).in_elevation = NEC_sites_num(k,6);
site.(site.codes{i}).species = unique(fns_part(:,3))';
for j = 1:length(site.(site.codes{i}).species)
if strcmp(site.(site.codes{i}).species{1,j},'co2')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CO2 X2007';
site.(site.codes{i}).species_standard_name{1,j} = 'carbon_dioxide';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppm';
site.(site.codes{i}).species_units{1,j} = 'micromol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
elseif strcmp(site.(site.codes{i}).species{1,j},'ch4')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CH4 X2004A';
site.(site.codes{i}).species_standard_name{1,j} = 'methane';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppb';
site.(site.codes{i}).species_units{1,j} = 'nanomol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
elseif strcmp(site.(site.codes{i}).species{1,j},'co')
site.(site.codes{i}).calibration_scale{1,j} = 'WMO CO X2014A';
site.(site.codes{i}).species_standard_name{1,j} = 'carbon_monoxide';
site.(site.codes{i}).species_units_long_name{1,j} = 'ppb';
site.(site.codes{i}).species_units{1,j} = 'nanomol mol-1';
site.(site.codes{i}).instrument{1,j} = 'Picarro G2301';
end
end
site.(site.codes{i}).country = 'United States';
site.(site.codes{i}).time_zone = 'America/New_York'; % use timezones to find out the available time zone designations.
site.(site.codes{i}).date_issued = date_issued;
site.(site.codes{i}).date_issued_str = datestr(site.(site.codes{i}).date_issued,'yyyy-mm-ddThh:MM:ssZ');
site.date_issued = max([site.date_issued,site.(site.codes{i}).date_issued]);
i = i+1;
end
%% Loading the data
for i = 1:length(site.codes)
for sp = 1:length(site.(site.codes{i}).species)
sptxt = site.(site.codes{i}).species{sp};
for inlet = 1:length(site.(site.codes{i}).inlet_height_long_name)
intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
site.(site.codes{i}).([sptxt,'_',intxt]) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = [];
site.(site.codes{i}).([sptxt,'_',intxt,'_files']) = dir(fullfile(readFolder,city,version_folder,[site.codes{i},'*',sptxt,'-',intxt,'*.csv']));
for fni = 1:length(site.(site.codes{i}).([sptxt,'_',intxt,'_files']))
fn = fullfile(site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).folder,site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).name);
if isempty(fn); fprintf('No file %s.\nContinuing onto the next file.\n',fn); keyboard; end
in_format = '%s%f%f%f%f%f%f%f%f%f%f%f%s';
fid = fopen(fn);
read_dat = textscan(fid,in_format,'HeaderLines',1,'Delimiter',',','CollectOutput',true,'TreatAsEmpty','NaN');
fclose(fid);
site.(site.codes{i}).([sptxt,'_',intxt]) = [site.(site.codes{i}).([sptxt,'_',intxt]); read_dat{1,2}(:,6)]; % CO2
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_std']); read_dat{1,2}(:,7)]; % CO2 std
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_n']); read_dat{1,2}(:,8)]; % CO2 n
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_unc']); read_dat{1,2}(:,11)]; % CO2 uncertainty
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = [site.(site.codes{i}).([sptxt,'_',intxt,'_time']); datetime(read_dat{1,1},'InputFormat','yyyy-MM-dd HH:mm:ss')]; % time
fprintf('File read: %s\n',site.(site.codes{i}).([sptxt,'_',intxt,'_files'])(fni).name)
end
% Removes the leading and trailing NaNs
data_range_ind = find(~isnan(site.(site.codes{i}).([sptxt,'_',intxt])),1,'first'):find(~isnan(site.(site.codes{i}).([sptxt,'_',intxt])),1,'last');
site.(site.codes{i}).([sptxt,'_',intxt]) = site.(site.codes{i}).([sptxt,'_',intxt])(data_range_ind);
site.(site.codes{i}).([sptxt,'_',intxt,'_std']) = site.(site.codes{i}).([sptxt,'_',intxt,'_std'])(data_range_ind);
site.(site.codes{i}).([sptxt,'_',intxt,'_n']) = site.(site.codes{i}).([sptxt,'_',intxt,'_n'])(data_range_ind);
site.(site.codes{i}).([sptxt,'_',intxt,'_unc']) = site.(site.codes{i}).([sptxt,'_',intxt,'_unc'])(data_range_ind);
site.(site.codes{i}).([sptxt,'_',intxt,'_time']) = site.(site.codes{i}).([sptxt,'_',intxt,'_time'])(data_range_ind);
clear data_range_ind
site.(site.codes{i}).([sptxt,'_',intxt,'_lat']) = repmat(site.(site.codes{i}).in_lat,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_lon']) = repmat(site.(site.codes{i}).in_lon,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']) = repmat(site.(site.codes{i}).in_elevation,length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']) = repmat(site.(site.codes{i}).inlet_height{inlet},length(site.(site.codes{i}).([sptxt,'_',intxt])),1);
% Set fill values:
site.(site.codes{i}).([sptxt,'_',intxt])(isnan(site.(site.codes{i}).([sptxt,'_',intxt]))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_std'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_std']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_n'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_n']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_unc'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_unc']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_lat'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_lat']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_lon'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_lon']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_elevation'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_elevation']))) = -9999.0;
site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height'])(isnan(site.(site.codes{i}).([sptxt,'_',intxt,'_inlet_height']))) = -9999.0;
site.groups = [site.groups; {[sptxt,'_',site.(site.codes{i}).code,'_',intxt]}];
site.species = [site.species; {sptxt}];
end
end
end
%% Optional plots to spot check the data.
%i = 4;
%site.(site.codes{i}).species
% clear('ax')
% for i = 1:length(site.codes)
% intxt = site.(site.codes{i}).inlet_height_long_name{1};
% figure(i); clf;
% for j = 1:length(site.(site.codes{i}).species)
% sptxt = site.(site.codes{i}).species{j}; pltxt = [sptxt,'_',intxt];
% mask = true(size(site.(site.codes{i}).(pltxt))); mask(site.(site.codes{i}).(pltxt)==-9999) = false;
% if sum(mask)==0; mask(mask==false) = true; end % if they're all false, make them true so the plotting works. Will show up as -9999 line.
% ax(i,j) = subplot(length(site.(site.codes{i}).species),1,j);
% plot(site.(site.codes{i}).([sptxt,'_',intxt,'_time'])(mask),site.(site.codes{i}).(pltxt)(mask))
% grid on; ylabel(replace(pltxt,'_',' ')); title(site.codes{i})
% end
% linkaxes(ax(i,:),'x')
% end
%% Temporary code to truncate all sites to Dec 31, 2019 for the 4/21 ORNL DAAC archive
for i = 1:length(site.codes)
for sp = 1:length(site.(site.codes{i}).species) % only doing CO2 for now.
sptxt = site.(site.codes{i}).species{sp};
for inlet = 1:length(site.(site.codes{i}).inlet_height_long_name)
intxt = site.(site.codes{i}).inlet_height_long_name{inlet};
mask = site.(site.codes{i}).([sptxt,'_',intxt,'_time'])<datetime(2020,1,1); % Mask for data before 2020-01-01
fields = {'','_std','_n','_unc','_time','_lat','_lon','_elevation','_inlet_height'};
for j = 1:length(fields)
site.(site.codes{i}).([sptxt,'_',intxt,fields{j}]) = site.(site.codes{i}).([sptxt,'_',intxt,fields{j}])(mask); % Apply the mask
end
end
end
end
%% Identify the netCDF files to create based on species.
site.unique_species = unique(site.species);
site.species_list = [];
for species_ind = 1:length(site.unique_species)
site.species_list = [site.species_list, site.unique_species{species_ind},' '];
end
site.species_list = strip(site.species_list); % Removes the last space
for j = 1:length(site.species)
if strcmp(site.species{j,1},'co2')
site.species_standard_name{j,1} = 'carbon dioxide';
elseif strcmp(site.species{j,1},'ch4')
site.species_standard_name{j,1} = 'methane';
elseif strcmp(site.species{j,1},'co')
site.species_standard_name{j,1} = 'carbon monoxide';
end
end
%% Creating the netCDF file
fprintf('Now creating the netCDF files.\n')
eval('co2usa_create_netCDF')